Doctoral Thesis

Využití metod hlubokého učení pro segmentaci a klasifikaci nádorů prsu v ultrazvukovém zobrazování

Final Thesis 12.98 MB Summary of Thesis 12.98 MB

Author of thesis: Ali Hamza

Acad. year: 2026/2027

Supervisor: Ing. Martin Mézl, Ph.D.

Reviewers: Ing. Jan Kubíček, Ph.D., doc. RNDr. Petr Matula, Ph.D.

Abstract:

Breast cancer is one of the leading causes of cancer-related mortality among women worldwide, where early and accurate diagnosis plays a decisive role in improving survival outcomes. Breast ultrasound imaging is widely adopted in clinical practice due to its nonionizing nature, real-time capability, cost-effectiveness, and suitability for dense breast tissue. However, ultrasound images are inherently affected by speckle noise, low contrast, heterogeneous tissue appearance, and operator dependency, which significantly limit diagnostic reliability. To address these challenges, this doctoral thesis proposes a robust, automated computer-aided diagnosis (CAD) framework for breast tumor analysis using deep learning and machine learning techniques. The proposed framework follows a threestage pipeline comprising lesion segmentation, deep learning-based feature extraction, and tumor classification. In the first stage, image preprocessing was performed using anisotropic diffusion filtering to suppress speckle noise while preserving lesion boundaries. Breast lesions are then segmented using an advanced U-Net++ architecture. Experimental evaluation on the BUSI dataset demonstrates that U-Net++ achieves a Dice similarity coefficient of 0.911 and a mean Intersection-over-Union (IoU) of 0.838, outperforming standard U-Net and Efficient U-Net models and providing superior boundary localization. In the second stage, deep learning-based feature extraction is performed using a lightweight MobileNetV2 architecture, selected after comparative evaluation with InceptionV3, EfficientNetB7, ResNet50, and VGG16. MobileNetV2 offers an optimal balance between discriminative feature representation and computational efficiency, making it suitable for real-time and resource-constrained clinical environments. In the final stage, multiple machine learning classifiers, including Artificial Neural Networks (ANN), Support Vector Machines (SVM), Random Forest (RF), K-Nearest Neighbors (KNN), and Long Short-Term Memory (LSTM) networks, are evaluated for benign, malignant, and normal tumor classification. Ablation analysis confirms the contribution of each pipeline component, with accuracy dropping to 91.2% without feature extraction and 88.70% without segmentation. The fully optimized framework achieves an overall classification accuracy of 96.58%, highlighting the cumulative benefit of preprocessing, segmentation, and deep feature learning.Furthermore, the thesis explores the use of a conditional Generative Adversarial Network (cGAN) for dataset augmentation. The GAN-enhanced classification model achieves an average cross-validation accuracy of 91.4% ± 1.2%, with malignant tumor recall reaching 93.1%, and demonstrates strong generalization on a separate real-image test set with 91.03% accuracy. Overall, the proposed CAD framework significantly reduces operator dependency, improves diagnostic robustness, and demonstrates strong potential for realtime clinical deployment. This work contributes a scalable, lightweight, and highperformance solution for breast ultrasound-based cancer diagnosis and provides a foundation for future extensions involving end-to-end learning, multimodal imaging, and clinically validated deployment.

Keywords:

Computer-aided diagnosis; Segmentation; Classification; Feature extraction; Conditional generative adversarial networks

Date of defence

14.09.2026

Result of the defence

Not defended (thesis was not successfully defended)

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Process of defence

Uchazeč komisi seznámil s průběhem svého výzkumu a výsledky uvedenými v dizertační práci, avšak prezentace nebyla vždy dostatečně jasná a přesvědčivá. Na dotazy oponentů reagoval jen částečně uspokojivě; zejména nedokázal dostatečně objasnit zásadní metodologické nejasnosti, konzistenci prezentovaných výsledků, způsob rozdělení dat a vyloučení možného úniku dat mezi trénovacími a testovacími soubory. Odpovědi na dotazy ostatních členů komise byly místy obecné a neposkytly dostatečnou oporu pro prezentované výsledky dizertační práce.

Language of thesis

English

Faculty

Department

Study programme

Biomedical Technologies and Bioinformatics (DPC-BTB)

Composition of Committee

doc. Ing. Radim Kolář, Ph.D. (předseda)
doc. Ing. Radovan Jiřík, Ph.D. (člen)
doc. RNDr. Petr Matula, Ph.D. (člen)
Ing. Jan Kubíček, Ph.D. (člen)
prof. Ing. Adam Herout, Ph.D. (člen)
Ing. Jiří Chmelík, Ph.D. (člen)

Supervisor’s report
Ing. Martin Mézl, Ph.D.

Ali Hamza began his Ph.D. studies in 2020. The start of his program was affected by restrictions and measures related to the COVID-19 pandemic. Despite all these restrictions, he quickly adapted to his new environment in a foreign country.
His research focused on the application of artificial intelligence techniques, particularly deep learning, in the field of medical image processing. Ultrasound images were selected as the specific application for his research.
He presented the foundation for his future dissertation during his state doctoral exam. Even at that time, the proposal was designed as a hybrid computer-assisted diagnostic system (CAD) for processing breast ultrasound images. This was the first use of such a pipeline for analyzing ultrasound images. After improvements, revisions and testing, this approach was successfully published in the journal IEEE Access (Q2).
His research was further shaped by internships at universities abroad, primarily at Otto von Guericke University in Magdeburg (Germany) and the Université de Technologie Belfort-Montbéliard (France), where he expanded his knowledge of generative adversarial networks (GANs). He then applied this knowledge to augment the dataset and make further adjustments to the algorithm. This formed the basis for an article in the journal BMC Medical Imaging (Q2), which has currently been resubmitted after the second round of peer review as a “minor revision” with only formal objections.
Third peer-reviewed article was prepared as a “review” that examines the use of AI methods in the field of automated diagnosis of breast ultrasound images. This article, published in the journal Computers Methods and Programs in Biomedicine Update (Q1), has currently completed the first round of peer review as a “major review” and will be revised at a later date.
In addition to his research activities, he was also active in teaching. He participated in teaching computer labs and lectures in course Computers and Programming.
Ali Hamza has published the main results of his dissertation as one first-atuhored paper in Q2 journal with other first-authored paper in Q2 which will be publish soon. The third paper is in the review process with possible publication by the end of the year. In addition to these articles, he also presented preliminary results at two international conferences. Based on his results and expertise, he was successful in the selection process for a postdoctoral position at the Department of Cell and Molecular Biology at Uppsala University (Sweden) in Professor Johan Elf’s team. His research will focus on the quantitative analysis of various microscopic images of bacterial colonies.
I value Ali Hamza as a skilled Ph.D. student and researcher in the field of ultrasound medical image analysis. I recommend the thesis for the defense.

Reviewer’s report
Ing. Jan Kubíček, Ph.D.

viz pdf
File inserted by the reviewer Size
Posudek oponenta [.pdf] 427,47 kB

Reviewer’s report
doc. RNDr. Petr Matula, Ph.D.

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File inserted by the reviewer Size
Posudek oponenta [.pdf] 811,00 kB

Responsibility: Mgr. et Mgr. Hana Odstrčilová